tbuckley/cabot-search huggingface dataset:
Abstract 3487: An atlas of substrate specificities for the human tyrosine kinome
Authors: Jared L. Johnson, Tomer M. Yaron, Lewis C. Cantley, Michael B. Yaffe, Benjamin E. Turk, Emily M. Huntsman, Peter V. Hornbeck
Journal: Cancer Research (2023)

Abstract Numerous physiological processes are governed by tyrosine phosphorylation. The protein tyrosine kinases that carry this out are dysregulated in a variety of cancers and are the targets of efficacious drugs. For most tyrosine kinases, we have a very limited understanding of their downstream signaling pathways and phosphorylation targets. Conversely, thousands of tyrosine phosphorylation events have so far been experimentally identified, and the overwhelming majority of these do not have an associated kinase. In this work, we have utilized peptide arrays to determine the substrate sequence specificity for the human tyrosine kinome, comprising 46 receptor tyrosine kinases, 32 nonreceptor tyrosine kinases, and 14 noncanonical tyrosine kinases. Nearly every kinase we profiled favored tyrosines that were positioned next to phosphorylated amino acids, indicating that PTM priming and crosstalk are general properties of the tyrosine kinome. Comparisons with C. elegans orthologs suggested that tyrosine kinase substrate motifs have remained conserved throughout metazoan evolution. When we computationally utilized our dataset to identify kinases for tyrosine substrates, our predictions were in strong accordance with published reports. When applied to high-throughput tyrosine phosphoproteomics datasets, we could decipher the kinases involved in cellular responses to growth factors, oncogenic mutations, and targeted inhibitors. Together, this work uncovers fundamental rules of substrate selection for nearly the entire human tyrosine kinome and provides a comprehensive resource for connecting tyrosine phosphorylation events with their kinases and signaling pathways. Citation Format: Jared L. Johnson, Tomer M. Yaron, Lewis C. Cantley, Michael B. Yaffe, Benjamin E. Turk, Emily M. Huntsman, Peter V. Hornbeck. An atlas of substrate specificities for the human tyrosine kinome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3487.
Abstract 1754: Targeting the mitochondrial protein MAGMAS increases sensitivity to docetaxel in neuroendocrine prostate cancer cells
Authors: Alfonso M. Durán, Christian H. Yoo, Jennifer D. Tran, Krystal Santiago, Adil S. Mohammed, Carlos A. Casiano, Frankis A. Almaguel
Journal: Cancer Research (2023)

Abstract Metastatic prostate cancer (PCa) is the leading cause of PCa-associated deaths and one of the leading causes of cancer mortality in men. Novel therapeutics, such as Prostate Specific Membrane Antigen (PSMA) ligand therapy, are emerging as effective treatment strategies for metastatic prostate cancer. However, neuroendocrine differentiated (NED) metastatic PCa, which lacks the PSMA antigen, is deprived of effective biomarkers for disease treatment. Magmas, a 13.8 kDa mitochondrial protein, imports nuclear-encoded mitochondrial proteins into the mitochondrial matrix. Magmas is overexpressed in several aggressive tumors, such as breast cancer, glioblastoma, and prostate cancer. When overexpressed, Magmas plays a role as a cytoprotective protein by acting as a reactive oxygen species (ROS) scavenger that maintains sufficient ROS levels to promote cell proliferation, but below the threshold levels that could lead to apoptosis. This study was designed to investigate the pro-survival and therapy-resistance functions of Magmas in PCa cells expressing NED markers. Predictively, we observed that the docetaxel (DTX)-resistant PC3-DR and DU145-DR PCa cell lines expressed significantly higher levels of Magmas compared to their drug-sensitive parental cell lines. We hypothesized that inhibiting Magmas reduces the aggressive properties of highly proliferative DTX- resistant metastatic PCa cell lines and re-sensitize them to DTX. Magmas knockdown in DTX-sensitive and DTX-resistant PC3 and DU145 cells in the presence of increasing DTX treatments enhanced sensitivity to DTX. Consistent with these results, pharmacological inhibition of Magmas with the novel BT#9 inhibitor in combination with increasing DTX concentrations also enhanced sensitivity to DTX in these cell lines. Additional studies using clonogenic assays, cell migration/invasion assays, and tumorsphere formation assays are currently underway to further establish Magmas as a potential therapeutic target to attenuate the aggressive properties of chemoresistant PCa cells. Lastly, we will investigate the diagnostic potential of Magmas as a biomarker for NED and BT#9 as an imaging/therapeutic-specific agent for NED. Citation Format: Alfonso M. Durán, Christian H. Yoo, Jennifer D. Tran, Krystal Santiago, Adil S. Mohammed, Carlos A. Casiano, Frankis A. Almaguel. Targeting the mitochondrial protein MAGMAS increases sensitivity to docetaxel in neuroendocrine prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1754.
Abstract 5855: Spatial transcriptomics deciphers the cellular society of advanced colorectal cancer
Authors: Masahiro Hashimoto, Yuki Ozato, Yusuke Nakano, Tadashi Abe, Yuichi Hisamastu, Takeo Toshima, Yusuke Yonemura, Mamoru Uemura, Takaaki Masuda, Hirofumi Yamamoto, Masaki Mori, Hidetoshi Eguchi, Yuichiro Doki, Koshi Mimori
Journal: Cancer Research (2023)

Abstract Introduction: In recent years, single-cell RNA sequencing (scRNA-seq) and high-dimensional spatial transcriptomics (ST-seq) have contributed significantly to our understanding of the tumor microenvironment (TME) in many cancers. This is essential for understanding the tumor-stromal crosstalk. Thus, integrating scRNA-seq data with ST-seq data will facilitate understanding intercellular communication in TMEs. Material and Method: We performed and combined ST-seq in CRC with public scRNA-seq. And, immunohistochemistry (IHC) (HLA-G, CD68, and SPP1) was performed on 20 CRC surgical specimens collected in our hospital. To verify this, we knocked out H2-M3 (HLA-G in humans) in mouse CRC cell lines (MC-38 cells) using the CRISPR/Cas9 system and examined H2-M3 KO tumor volume in xenograft mouse models. Results: We identified co-localized cells with CRC cells at the invasive front and those in the center based on the spatial distribution estimated by an analytical pipeline, Cell2location. At the invasive front, CRC cells co-localized more frequently with SPP1+ macrophages than other cells. To dissect the molecular machinery and cell types inducing SPP1+ macrophages, we found ligand activity by another pipeline, NicheNet. The prominent signal to SPP1+ macrophages was mediated by several ligand-receptor pairs including HLA-G- immunoglobulin-like transcript (ILT)2/ILT4. Next, we disclosed the effect on CD8+ cells, and SPP1+ macrophages secrete IL-10 suppressing the immune activity of CD8+ T cells. And the ratio of HLA-G-positive cancer cells was predominantly higher in areas with more SPP1+ macrophages by IHC in CRC. In vivo analysis, H2-M3 KO reduced CRC tumor volume and tumor tissue from H2-M3 KO cells exhibited higher SPP1 and CD68 staining compared with wild type cells. Conclusion: SPP1+ macrophages and cancer cells secreting high levels of HLA-G may represent targets to improve the prognosis of patients with CRC. Further analysis is currently underway with a focus on early-stage cancer in carcinoma in adenoma. Citation Format: Masahiro Hashimoto, Yuki Ozato, Yusuke Nakano, Tadashi Abe, Yuichi Hisamastu, Takeo Toshima, Yusuke Yonemura, Mamoru Uemura, Takaaki Masuda, Hirofumi Yamamoto, Masaki Mori, Hidetoshi Eguchi, Yuichiro Doki, Koshi Mimori. Spatial transcriptomics deciphers the cellular society of advanced colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5855.
Abstract 3415: Preclinical characterization of a brain penetrant RAF inhibitor, BDTX-4933, targeting oncogenic BRAF Class I/II/III and RAS mutations
Authors: Yoon-Chi Han, Pui-Yee Ng, Luisa Shin Ogawa, Shao Ning Yang, Miao Chen, Noboru Ishiyama, Tai-An Lin, Elizabeth Buck
Journal: Cancer Research (2023)

Abstract Mutations in BRAF and RAS are often oncogenic and lead to a constitutively active MAPK pathway that promotes aberrant cell proliferation and tumor growth. Currently approved BRAF inhibitors are selective against monomeric BRAF V600 mutants. These drugs are largely inactive against non-V600 dimeric BRAF mutants and have poor brain penetration. Although there is an FDA-approved KRAS G12C mutant-selective inhibitor, there are no approved inhibitors for cancer patients who harbor other (non-G12C) KRAS and NRAS mutations which promote tumor growth likely through constitutively active RAF dimers. There remains a high unmet clinical need for a highly CNS penetrant oral RAF inhibitor that targets a broad spectrum of BRAF mutations and constitutively active RAF dimers without paradoxical activation of the MAPK signaling pathway. BDTX-4933 is a potent, reversible, CNS penetrant RAF MasterKey inhibitor designed to target a large family of oncogenic BRAF mutations including BRAF monomers and RAF dimers. The compound inhibits not only all classes (I, II, and III) of BRAF mutations but also targets constitutively active RAF dimers promoted by upstream oncogenic MAPK pathway alterations, such as RAS mutations. In a panel of cancer cell lines that endogenously express BRAF or RAS mutations, BDTX-4933 demonstrates inhibition of the MAPK pathway signaling without paradoxical activation, resulting in potent inhibition of cellular proliferation. BDTX-4933 shows target engagement, inhibiting ERK phosphorylation, in tumor models in vivo, achieving strong anti-tumor efficacy and tumor regression across tumor models driven by either BRAF or RAS mutations. Furthermore, BDTX-4933 exhibits high CNS exposure leading to dose-dependent tumor growth inhibition, and survival benefit in mice implanted intracranially with xenograft BRAF mutant tumors. BDTX-4933 has a best-in-class profile to treat cancer patients harboring BRAF mutations or RAF dimer-promoting upstream genetic alterations. IND-enabling studies for BDTX-4933 are on-going. Citation Format: Yoon-Chi Han, Pui-Yee Ng, Luisa Shin Ogawa, Shao Ning Yang, Miao Chen, Noboru Ishiyama, Tai-An Lin, Elizabeth Buck. Preclinical characterization of a brain penetrant RAF inhibitor, BDTX-4933, targeting oncogenic BRAF Class I/II/III and RAS mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3415.
Abstract 3629: Calcium signalling and the breast cancer microenvironment
Authors: Alice H. Bong, Krystyna A. Gieniec, Francisco Sadras, Mélanie Robitaille, Sarah J. Roberts-Thomson, Felicity M. Davis, Gregory R. Monteith
Journal: Cancer Research (2023)

Abstract Calcium is a key regulator of a variety of pathways important in breast cancer progression, including those involved in cell proliferation and invasiveness. Calcium signaling is implicated in processes relevant to the breast cancer tumor microenvironment and altered calcium influx is a feature of cancer associated fibroblasts. In these studies, simultaneous use of genetically encoded calcium indicators with distinct fluorescence spectral properties (GCaMP6m or JRCaMP1b), were used to explore the cross-talk between breast cancer cells and fibroblasts via calcium signaling and changes in different cellular compartments. HMF3S human fibroblast cells co-cultured with breast cancer cells expressing GCaMP6m or JRCaMP1b were assessed in 2D and 3D co-culture using automated epi-fluorescence or confocal microscopy. Mitochondrial calcium levels were assessed using targeted GCaMP6m (2mtGCaMP6m) in HMF3S cells expressing JRCaMP1b. Results showed distinct spatial and temporal changes in free calcium levels between both fibroblasts and breast cancer cells and the mitochondria and cytosol during activation. These methodological advances provide an opportunity to better understand calcium signaling in cancer associated fibroblasts. These techniques will also help identify the calcium channels and pumps that could be targeted to manipulate the breast cancer tumor microenvironment to inhibit pathways important in breast cancer progression. Citation Format: Alice H. Bong, Krystyna A. Gieniec, Francisco Sadras, Mélanie Robitaille, Sarah J. Roberts-Thomson, Felicity M. Davis, Gregory R. Monteith. Calcium signalling and the breast cancer microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3629.
Abstract 4754: Investigating the impact of hotspot mutations in a chromatin reader on leukemogenesis
Authors: Yiman Liu, Qinglan Li, Sylvia Tang, Chujie Gong, Liling Wan
Journal: Cancer Research (2023)

Abstract Acute myeloid leukemia (AML) is one of the most aggressive forms of hematological malignancies with a low overall 5-year survival rate (&amp;lt; 26%). The mainstay of treatment for AML includes chemotherapy, but the response of a subset of patients to current treatment options remains poor. Thus, new therapeutic approaches are desperately needed. AML often arises from somatic mutations in chromatin regulators that result in uncontrolled proliferation and a block of differentiation in myeloid progenitor cells. As such, investigation of the role and molecular mechanism of chromatin regulator in AML is being actively pursued. Previously, we discovered the eleven-nineteen-leukemia (ENL) protein, a chromatin “reader” and transcription co-activator, as an unrecognized requirement for the survival of AML. We developed a potent and orally bioavailable small-molecule inhibitor of ENL, which displaces ENL from chromatin and blocks AML progression. Hotspot mutations have been found in ENL YEATS domains, both in Wilms tumor and in leukemia, and these mutations confer a gain of condensation property, leading to aberrant gene activation. However, the impact of ENL mutation on tumorigenesis is largely unknown. The over-arching goal of this project is to explore the impact of the hyper-activated ENL pathway (ENL mutation) in AML. Results from this project will elucidate how newly discovered chromatin reader mutations drive tumorigenesis and offer new biology insights that will facilitate both basic mechanistic studies and clinical studies. Citation Format: Yiman Liu, Qinglan Li, Sylvia Tang, Chujie Gong, Liling Wan. Investigating the impact of hotspot mutations in a chromatin reader on leukemogenesis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4754.
Abstract 337: Antitumor effect of oncomagnetic therapy in glioblastoma
Authors: Arvind Pandey, Shashank Hambarde, David S. Baskin, Santosh A. Helekar
Journal: Cancer Research (2023)

Abstract Background: Glioblastoma (GBM) is the most lethal primary malignant brain tumor with a median survival of 15-20 months. Concurrent temozolomide (TMZ) chemotherapy and radiation (XRT) remain the current standard of care (SOC) treatment for newly diagnosed GBM. The addition of tumor treating fields (TTFs) improves median survival from 16 to 20.9 months. This modest improvement underscores the urgent need to identify a new treatment modality as standalone therapy. We have reported recently that brief 2 - 6 h of daily brain stimulation with a new noninvasive, non-contact, magnetic stimulation device causes &amp;gt;30% reduction of contrast-enhanced tumor (CET) volume in an end-stage recurrent GBM patient after a ~30-day treatment. Purpose: The noninvasive Oncomagnetic device developed in our laboratory selectively kills glioblastoma (GBM) and other cancer cells while sparing normal developing neurons and astrocytes in vitro. The spinning oscillating magnetic field (sOMF) generated by this device disrupts electron transport in the mitochondrial respiratory chain leading to a marked increase in reactive oxygen species (ROS) and consequent cancer cell death. However, the downstream molecular mechanism of sOMF action is under investigation. We studied the cellular and molecular effects of sOMF treatment on GBM cell lines and investigated the response to Oncomagnetic monotherapy (OMT) in a syngeneic mouse model. We treated LN229 and U87 GBM cells with sOMF with and without a sub-therapeutic dose of TMZ in vitro. To study the anticancer effect of sOMF in vivo, we developed syngeneic GBM tumors in BALB/c mice by stereotactic intracranial injection of GL261WT cells. Tumor growth was monitored periodically by MRI scans. Results: Our results showed that sOMF significantly reduce cell proliferation and cell survival in vitro. We observed that sOMF induces DNA damage and arrests cells in G1 phase of cell cycle. OMT of tumor-bearing mice using a whole-body sOMF stimulation method caused a substantial retardation of tumor growth and reduction of the contrast-enhanced tumor volume in 9.4 T MRI scans. OMT also showed significant increase in overall survival in these mice. Conclusion: These experiments contribute to unraveling the mechanism of action underlying the response to OMT in GBM and provide a strong rationale for a standalone Oncomagnetic therapy for GBM. Citation Format: Arvind Pandey, Shashank Hambarde, David S. Baskin, Santosh A. Helekar. Antitumor effect of oncomagnetic therapy in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 337.
Abstract 6692: Identification of circulating tumor cells based on machine learning
Authors: Jae Hyuk Lee, Sung Ho Park, Jihoon Kang, Jihyun Lee, Soee Kim, Jungwon Kim, Young Woong Sohn, Jong Kil Lee
Journal: Cancer Research (2023)

Abstract Circulating tumor cells (CTC) are tumor cells that have shed into the bloodstream from primary tumor and circulate in the blood. CTC could provide better understanding of tumor metastasis and show the possibility as promising biomarker for early detection of cancer, cancer prognosis, noninvasive monitoring of treatment response, and personalized medicine. However, the isolation and characterization has been a major technological challenge due to their rareness among the massive blood cells. CytoGen’s Smart BiopsyTM CTC platform comprised of CTC isolator, IF (Immunofluorescence) Stainer, and Cell Image Analyzer is a unique and competitive technology platform for the isolation and analysis of CTC from blood. Intact live CTC could be isolated gravity-based filtration via high-density micro-porous (HDM) chip with minimized cellular damage and high retrieval rate. For the more accurate and quick analysis of CTC after isolation with Smart BiopsyTM CTC platform, we are developing the analysis method of CTC identification using machine learning technologies. Preliminary results of machine learning showed the accurate separation of CTC and PBMC (peripheral blood mononuclear cells) based on the specific markers of them. CTC identification based on machine learning technologies might be reliable analysis method and give secure information of CTC. Citation Format: Jae Hyuk Lee, Sung Ho Park, Jihoon Kang, Jihyun Lee, Soee Kim, Jungwon Kim, Young Woong Sohn, Jong Kil Lee. Identification of circulating tumor cells based on machine learning. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6692.
Abstract 2322: Precision immuno-oncology (IO) ISH/IF multiplex panel: Spatial detection of cytokines and IO biomarkers
Authors: Brenna Dennison, Stephanie Allen, Bhavika Patel, Jacob Stapleton, Roni Archuleta, Mary Lou Rath, Navi Mehra, Sameer S. Talwalkar
Journal: Cancer Research (2023)

Abstract Cytokines have a large impact on the tumor microenvironment by affecting cell growth, survival, inflammation, and differentiation. Understanding the spatial biology within the tumor microenvironment, including the cytokine organization within specific cell types, can lead to better treatment plans for patients. We developed a hybrid multiplex panel, using RNA in-situ hybridization (ISH) and immunofluorescence (IF) to investigate the spatial biology of the tumor microenvironment. This panel also enabled us to simultaneously detect the RNA of cytokines and protein of specific immuno-oncology (IO) biomarkers. This allows us to visualize spatially, not only the organization of cell types but also to identify the cellular sources of specific cytokines. In this study, we analyzed the tumor microenvironment of samples from non-small cell lung cancer (NSCLC) and breast cancer in two panels for cytokine RNAs and IO protein biomarkers. Panel 1 included TNFa and IL-2 cytokines combined with the CD68 and CD163 IO protein biomarkers. Panel 2 consisted of IL-6 and IL-2 cytokines with the PAX5 and CD3 IO protein biomarkers. Staining was completed on the Leica Bond RX autostainer, and slides were scanned using the PhenoImager™ Fusion. Visiopharm® software was used to analyze the tumor microenvironment of tissue samples and localize cytokines in specific cell types. CD163 positive macrophages (M2 phenotype) were seen predominantly within the tumors (NSCLC and breast cancer) whereas CD68 positive macrophages were identified towards the periphery in the non-tumor microenvironment. NSCLC tumor cells showed higher expression levels of IL-2, IL-6 and TNFa compared to breast cancer tumor cells. Predominance of CD3 positive T cells was noted with relative lack of PAX5 positive B cells within both NSCLC and breast cancer tumors. Multiplexing enabled assessment of relative expression levels of IL-2, IL-6 and TNFa in T lymphocytes and macrophages and TNFa in dendritic cells. Our hybrid multiplex panel can provide insights into the visualization of spatial organization of tumor microenvironment. It also enables semi-quantitative assessments for the expression levels of cytokines and their relative expression within tumor and immune cells, thereby helping to correlate response to treatment, especially with checkpoint inhibitors. Citation Format: Brenna Dennison, Stephanie Allen, Bhavika Patel, Jacob Stapleton, Roni Archuleta, Mary Lou Rath, Navi Mehra, Sameer S. Talwalkar. Precision immuno-oncology (IO) ISH/IF multiplex panel: Spatial detection of cytokines and IO biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2322.